Mesh Cleanup - Self Intersection and Dual Face Removal
Your mesh is pretty simple, I would recommend to repair it manually.

Here’s how I’d do it.
The repaired Blendfile is attached at the end.

1) Set units to milimetres and snapping to Increments.
Enable absolute grid snap. This will make it waaay easier to achieve accurate results.
It’s very useful for precise modeling (like for 3D printing) 





2) Remove half of your mesh. Because it’s symmetrical, we’ll work only on one half, and generate the other one automatically.
- Also remove all the overlapping end faces
- The middle part was kinda messed up, so I repaired it manually. It was easy, try it for yourself.

I’ve put the repaired mesh into the blender file for you. Use it to follow the next steps.
You’re welcome :).



3) Add two loopcuts. Don’t worry about an exact position, you can adjust it later.  



4) Select faces you don’t need and delete them. Press Delete->Faces



5) Select the four vertices on top and Press F to fill.
Do the same thing for the bottom four vetices.




6) Select the front loop by clicking Alt+LMB on a vertex and Press F to fill.
Do the same for the back loop.

 


7) You’re almost done.
Now you have a perfect half of your handle.  

Now select the mesh and Click RMB->Set Origin to 3Dcursor. This is gonna be important in the next step. 



7.1) Correct normals
Click Overlay->Face orientation to show the normals.
Red faces should be inside, blue on the outside.  

Select all faces with Select->All and go to Mesh->Normals->Recalculate Outside. Blender will then recalculate them correctly.

You can see some inverted normals in your original mesh.


8) Add a mirror modifier.
Set the correct axis (Y in this example).

 

9) You can select the loop (use X-ray mode), and move it up or down as you like.
The other half of your mesh will adjust itself.



10) Done.
You’ve got a clean mesh without any non-planar or overlapping faces.

Repaired Blender file
- Includes the end result
- Includes the Step 01 mesh.


Aaaaaah.
God damn, that took longer than I expected.

Additional tips:
- Apply all modifiers before exporting file for 3D printer
- Check BlenderGuru for basic Blender tutorials
- You’re doing great, happy Blendering